Evidence for ARGONAUTE4–DNA interactions in RNA-directed DNA methylation in plants

RNA polymerase V (Pol V) long noncoding RNAs (lncRNAs) have been proposed to guide ARGONAUTE4 (AGO4) to chromatin in RNA-directed DNA methylation (RdDM) in plants. Here, we provide evidence, based on laser UV-assisted zero-length cross-linking, for functionally relevant AGO4–DNA interaction at RdDM targets. We further demonstrate that Pol V lncRNAs or the act of their transcription are required to lock Pol V holoenzyme into a stable DNA-bound state that allows AGO4 recruitment via redundant glycine–tryptophan/tryptophan–glycine AGO hook motifs present on both Pol V and its associated factor, SPT5L. We propose a model in which AGO4–DNA interaction could be responsible for the unique specificities of RdDM.